121
metabolomics, transcriptomics, ionomics), conventionalizes the application
of systems biology in seagrasses (Nicholson and Wilson 2003). The integration of constantly developing computer algorithms with experimental data
will potentially produce mathematical models of such biological systems
(Hiroaki 2002). As long as this biological information is enriched, the gap
between the mathematical models and the observed data will converge. Along
these lines, it becomes feasible to integrate molecular functions, their interactions, the molecular pathways, the networks they participate in, and the
dynamics among networks. This kind of data requires high-quality datasets,
available computational methods, and high-level computational capacity.
Finally, all these pieces of information need vastly available databases for
comparative analysis of such biological networks.
6.2.1 Genomics
Seagrasses have evolved from terrestrial plants and exhibit a spectacular repertoire
of adaptation mechanisms in order to survive submerged in the marine environment.
Seagrasses settled in the sea about 100 million years ago (Hemminga and Duarte
2000) and belong in 5 monocotyledon families, containing 12 genera. This evolutionary pathway has provoked alterations in genes and genomes that reflect the ability of seagrasses to develop and grow in aquatic environments. For example, the
photosynthetic process is differentiated according to depth gradient, and epiphytes
usually cover a large part of the photosynthetically active leaves of the plants (Dalla
Via et al. 1998). Wissler et al. (2011) identified in seagrasses 51 genes as positively
selected, belonging in a few metabolic pathways, photosynthesis, and translation
machinery (ribosomes), which diverged after the split of the common ancestor from
terrestrial monocotyledonous plants. Transcriptomic analysis in Zostera muelleri
suggested that genes involved in ethylene metabolism and signaling functions are
missing and that there is a gene loss in processes related with ethylene biosynthesis
and signaling in the species in question (Golicz et al. 2015).
The introduction of state-of-the-art genomic technologies in seagrass studies
motivated groundbreaking advances, resulting in novel scientific fields. Genomic
inventions deliver fast, inexpensive, and accurate genome information, having tremendous advantages over conventional methods. The development of such new
technologies applied to molecular biology and genomics, such as next-generation
sequencing methods and high-throughput genotyping, allows the rapid increase of
availability of genomic resources in seagrasses. These resources will provide valuable insights to the research community and will help in the determination of the
genetic factors involved in several biological aspects of seagrass species.
Bioinformatics analyses are being made easier as the quantity of the available software is increased and the annotations provided by databases are continuously
improving, especially for terrestrial plants. Available depositories are enriched in a
daily basis, and an extensive usage of databases such as UniProt, Nr, and RefSeq is
6 Abiotic Stress of Seagrasses
metabolomics, transcriptomics, ionomics), conventionalizes the application
of systems biology in seagrasses (Nicholson and Wilson 2003). The integration of constantly developing computer algorithms with experimental data
will potentially produce mathematical models of such biological systems
(Hiroaki 2002). As long as this biological information is enriched, the gap
between the mathematical models and the observed data will converge. Along
these lines, it becomes feasible to integrate molecular functions, their interactions, the molecular pathways, the networks they participate in, and the
dynamics among networks. This kind of data requires high-quality datasets,
available computational methods, and high-level computational capacity.
Finally, all these pieces of information need vastly available databases for
comparative analysis of such biological networks.
6.2.1 Genomics
Seagrasses have evolved from terrestrial plants and exhibit a spectacular repertoire
of adaptation mechanisms in order to survive submerged in the marine environment.
Seagrasses settled in the sea about 100 million years ago (Hemminga and Duarte
2000) and belong in 5 monocotyledon families, containing 12 genera. This evolutionary pathway has provoked alterations in genes and genomes that reflect the ability of seagrasses to develop and grow in aquatic environments. For example, the
photosynthetic process is differentiated according to depth gradient, and epiphytes
usually cover a large part of the photosynthetically active leaves of the plants (Dalla
Via et al. 1998). Wissler et al. (2011) identified in seagrasses 51 genes as positively
selected, belonging in a few metabolic pathways, photosynthesis, and translation
machinery (ribosomes), which diverged after the split of the common ancestor from
terrestrial monocotyledonous plants. Transcriptomic analysis in Zostera muelleri
suggested that genes involved in ethylene metabolism and signaling functions are
missing and that there is a gene loss in processes related with ethylene biosynthesis
and signaling in the species in question (Golicz et al. 2015).
The introduction of state-of-the-art genomic technologies in seagrass studies
motivated groundbreaking advances, resulting in novel scientific fields. Genomic
inventions deliver fast, inexpensive, and accurate genome information, having tremendous advantages over conventional methods. The development of such new
technologies applied to molecular biology and genomics, such as next-generation
sequencing methods and high-throughput genotyping, allows the rapid increase of
availability of genomic resources in seagrasses. These resources will provide valuable insights to the research community and will help in the determination of the
genetic factors involved in several biological aspects of seagrass species.
Bioinformatics analyses are being made easier as the quantity of the available software is increased and the annotations provided by databases are continuously
improving, especially for terrestrial plants. Available depositories are enriched in a
daily basis, and an extensive usage of databases such as UniProt, Nr, and RefSeq is
6 Abiotic Stress of Seagrasses